Advise Needed: Pricing extra's & add ins

My current POS had some updates and one of them was for modifiers on drinks and foods. It is asking me the separate charge for "add", "extra" "no" "light" etc. So it made me realize that it has been a while since I checked my pricing.
Lately we have been selling a LOT of paleo drinks and our customers are asking for honey. We use a more expensive local raw honey and since we haven't charged for that in the past, I have been losing money on some drinks.

At what cost do you mark up your extra shots, flavors, etc?

Typically I have that figured into the cost of the drink, and when they want extra flavor we charge .65 just because that was the going price when we started.

I'm going to add honey as a modifier and charge if they want it as an extra that is not already figured into the drink. If the honey costs me .36 cents an ounce, would I charge just enough to cover my cost or would I actually try to get it into the 30% - 35% range?
What do you typically do for your extra's and add in's?
Thanks in advance for any input!

In the cafe's where I've worked in past years, the charge for extras (shots of flavor or chocolate syrup) that people want added, have been .50 - simply because it is a nice, round number.
When people ask for honey, we don't have it as an add on - but there is a display of honey sticks that they can buy (3 for $1) to squeeze the honey into their drinks by themselves. We tried having honey on the condiment table in the café (the squeeze bottles) but people actually would walk off with them. I imagine their coat pockets being pretty sticky by the time they get home.